1
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Palmioli A, Airoldi C. An NMR Toolkit to Probe Amyloid Oligomer Inhibition in Neurodegenerative Diseases: From Ligand Screening to Dissecting Binding Topology and Mechanisms of Action. Chempluschem 2024:e202400243. [PMID: 38712695 DOI: 10.1002/cplu.202400243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/03/2024] [Accepted: 05/06/2024] [Indexed: 05/08/2024]
Abstract
The aggregation of amyloid peptides and proteins into toxic oligomers is a hallmark of neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, Machado-Joseph's disease, and transmissible spongiform encephalopathies. Inhibition of amyloid oligomers formation and interactions with biological counterparts, as well as the triggering of non-toxic amorphous aggregates, are strategies towards preventive interventions against these pathologies. NMR spectroscopy addresses the need for structural characterization of amyloid proteins and their aggregates, their binding to inhibitors, and rapid screening of compound libraries for ligand identification. Here we briefly discuss the solution experiments constituting the NMR spectroscopist's toolkit and provide examples of their application.
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Affiliation(s)
- Alessandro Palmioli
- Department of Biotechnology and Biosciences, University of Milano - Bicocca, P.zza della Scienza 2, 20126, Milan, Italy
| | - Cristina Airoldi
- Department of Biotechnology and Biosciences, University of Milano - Bicocca, P.zza della Scienza 2, 20126, Milan, Italy
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2
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Palmioli A, Moretti L, Vezzoni CA, Legnani L, Sperandeo P, Baldini L, Sansone F, Airoldi C, Casnati A. Multivalent calix[4]arene-based mannosylated dendrons as new FimH ligands and inhibitors. Bioorg Chem 2023; 138:106613. [PMID: 37224739 DOI: 10.1016/j.bioorg.2023.106613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/05/2023] [Accepted: 05/11/2023] [Indexed: 05/26/2023]
Abstract
We report the synthesis and biological characterization of a novel class of multivalent glycoconjugates as hit compounds for the design of new antiadhesive therapies against urogenital tract infections (UTIs) caused by uropathogenic E. coli strains (UPEC). The first step of UTIs is the molecular recognition of high mannose N-glycan expressed on the surface of urothelial cells by the bacterial lectin FimH, allowing the pathogen adhesion required for mammalian cell invasion. The inhibition of FimH-mediated interactions is thus a validated strategy for the treatment of UTIs. To this purpose, we designed and synthesized d-mannose multivalent dendrons supported on a calixarene core introducing a significant structural change from a previously described family of dendrimers bearing the same dendrons units on a flexible pentaerythritol scaffold core. The new molecular architecture increased the inhibitory potency against FimH-mediated adhesion processes by about 16 times, as assessed by yeast agglutination assay. Moreover, the direct molecular interaction of the new compounds with FimH protein was assessed by on-cell NMR experiments acquired in the presence of UPEC cells.
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Affiliation(s)
- Alessandro Palmioli
- BioOrg NMR Lab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.zza della Scienza, 2, 20126 Milan, Italy
| | - Luca Moretti
- BioOrg NMR Lab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.zza della Scienza, 2, 20126 Milan, Italy
| | - Carlo Alberto Vezzoni
- Department of Chemistry, Life Sciences and Environmental Sustainability, Parco Area delle Scienze 17/a, 43124 Parma, Italy
| | - Laura Legnani
- BioOrg NMR Lab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.zza della Scienza, 2, 20126 Milan, Italy
| | - Paola Sperandeo
- Department of Pharmacological and Biomolecular Sciences, University of Milano, Via Balzaretti, 9/11/13, 20133 Milano, Italy
| | - Laura Baldini
- Department of Chemistry, Life Sciences and Environmental Sustainability, Parco Area delle Scienze 17/a, 43124 Parma, Italy
| | - Francesco Sansone
- Department of Chemistry, Life Sciences and Environmental Sustainability, Parco Area delle Scienze 17/a, 43124 Parma, Italy
| | - Cristina Airoldi
- BioOrg NMR Lab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.zza della Scienza, 2, 20126 Milan, Italy.
| | - Alessandro Casnati
- Department of Chemistry, Life Sciences and Environmental Sustainability, Parco Area delle Scienze 17/a, 43124 Parma, Italy.
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3
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Palmioli A, Sperandeo P, Bertuzzi S, Polissi A, Airoldi C. On-cell saturation transfer difference NMR for the identification of FimH ligands and inhibitors. Bioorg Chem 2021; 112:104876. [PMID: 33845337 DOI: 10.1016/j.bioorg.2021.104876] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/14/2021] [Accepted: 03/25/2021] [Indexed: 12/23/2022]
Abstract
We describe the development of an on-cell NMR method for the rapid screening of FimH ligands and the structural identification of ligand binding epitopes. FimH is a mannose-binding bacterial adhesin expressed at the apical end of type 1 pili of uropathogenic bacterial strains and responsible for their d-mannose sensitive adhesion to host mammalian epithelial cells. Because of these properties, FimH is a key virulence factor and an attractive therapeutic target for urinary tract infection. We prepared synthetic d-mannose decorated dendrimers, we tested their ability to prevent the FimH-mediated yeast agglutination, and thus we used the compounds showing the best inhibitory activity as models of FimH multivalent ligands to set up our NMR methodology. Our experimental protocol, based on on-cell STD NMR techniques, is a suitable tool for the screening and the epitope mapping of FimH ligands aimed at the development of new antiadhesive and diagnostic tools against urinary tract infection pathogens. Notably, the study is carried out in a physiological environment, i.e. at the surface of living pathogen cells expressing FimH.
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Affiliation(s)
- Alessandro Palmioli
- BioOrg NMR Lab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.zza della Scienza, 2, 20126 Milan, Italy.
| | - Paola Sperandeo
- Department of Pharmacological and Biomolecular Sciences, University of Milano, Via Balzaretti, 9/11/13, 20133 Milano, Italy
| | - Sara Bertuzzi
- BioOrg NMR Lab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.zza della Scienza, 2, 20126 Milan, Italy; Chemical Glycobiology Lab, Center for Cooperative Research in Biosciences (CIC-bioGUNE), 48160 Derio, Spain
| | - Alessandra Polissi
- Department of Pharmacological and Biomolecular Sciences, University of Milano, Via Balzaretti, 9/11/13, 20133 Milano, Italy
| | - Cristina Airoldi
- BioOrg NMR Lab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.zza della Scienza, 2, 20126 Milan, Italy.
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4
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Kijek TM, Bozue JA, Panchal RG, Litosh VA, Woodard RW, Ahmed SA. A direct spectropolarimetric assay of arabinose 5-phosphate isomerase. Anal Biochem 2021; 622:114116. [PMID: 33716126 DOI: 10.1016/j.ab.2021.114116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 12/20/2020] [Accepted: 01/18/2021] [Indexed: 10/21/2022]
Abstract
Arabinose 5-phosphate isomerase (API) catalyzes the reversible isomerization of Ribulose 5-phosphate (Ru5P) to Arabinose 5-Phosphate (Ar5P) for the production of 3-deoxy-2-octulosonic acid 8-phosphate (KDO), a component of bacterial lipopolysaccharide (LPS) of gram-negative bacteria. API is an attractive target for therapeutic development against gram-negative bacterial pathogens. The current assay method of API activity utilizes a general reaction for keto sugar determination in a secondary, 3-h color development reaction with 25 N sulfuric acid which poses hazard to both personnel and instrumentation. We therefore aimed to develop a more user friendly assay of the enzyme. Since Ru5P absorbs in the UV region and contains at least 2 chiral centers, it can be expected to display circular dichroism (CD). A wavelength scan revealed indeed Ru5P displays a pronounced negative ellipticity of 30,560 mDeg M-1cm-1 at 279 nm in Tris buffer pH 9.1 but Ar5P does not have any CD. API enzymatic reactions were monitored directly and continuously in real time by following the disappearance of CD from the Ru5P substrate, or by the appearance of CD from Ar5P substrate. The CD signal at this wavelength was not affected by absorption of the enzyme protein or of small molecules, or turbidity of the solution. Common additives in protein and enzyme reaction mixtures such as detergents, metals, and 5% dimethylsulfoxide did not interfere with the CD signal. Assay reactions of 1-3 min consistently yielded reproducible results. Introduction of accessories in a spectropolarimeter will easily adapt this assay to high throughput format for screening thousands of small molecules as inhibitor candidates of API.
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Affiliation(s)
- Todd M Kijek
- Systems and Structural Biology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, 21702, USA
| | - Joel A Bozue
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, 21702, USA
| | - Rekha G Panchal
- Systems and Structural Biology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, 21702, USA
| | - Vladislav A Litosh
- Medical Countermeasures Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, 21702, USA
| | - Ronald W Woodard
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109-1065, USA
| | - S Ashraf Ahmed
- Systems and Structural Biology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, 21702, USA.
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5
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On-cell saturation transfer difference NMR study of Bombesin binding to GRP receptor. Bioorg Chem 2020; 99:103861. [PMID: 32339813 DOI: 10.1016/j.bioorg.2020.103861] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 04/15/2020] [Accepted: 04/16/2020] [Indexed: 01/15/2023]
Abstract
We report the NMR characterization of the molecular interaction between Gastrin Releasing Peptide Receptor (GRP-R) and its natural ligand bombesin (BN). GRP-R is a transmembrane G-protein coupled receptor promoting the stimulation of cancer cell proliferation; in addition, being overexpressed on the surface of different human cancer cell lines, it is ideal for the development of new strategies for the selective targeted delivery of anticancer drugs and diagnostic devices to tumor cells. However, the design of new GRP-R binders requires structural information on receptor interaction with its natural ligands. The experimental protocol presented herein, based on on-cell STD NMR techniques, is a powerful tool for the screening and the epitope mapping of GRP-R ligands aimed at the development of new anticancer and diagnostic tools. Notably, the study can be carried out in a physiological environment, at the surface of tumoral cells overespressing GRP-R. Moreover, to the best of our knowledge, this is the first example of an NMR experiment able to detect and investigate the structural determinants of BN/GRP-R interaction.
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Vacchini M, Edwards R, Guizzardi R, Palmioli A, Ciaramelli C, Paiotta A, Airoldi C, La Ferla B, Cipolla L. Glycan Carriers As Glycotools for Medicinal Chemistry Applications. Curr Med Chem 2019; 26:6349-6398. [DOI: 10.2174/0929867326666190104164653] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 11/07/2018] [Accepted: 12/18/2018] [Indexed: 12/12/2022]
Abstract
Carbohydrates are one of the most powerful and versatile classes of biomolecules that nature
uses to regulate organisms’ biochemistry, modulating plenty of signaling events within cells, triggering
a plethora of physiological and pathological cellular behaviors. In this framework, glycan carrier
systems or carbohydrate-decorated materials constitute interesting and relevant tools for medicinal
chemistry applications. In the last few decades, efforts have been focused, among others, on the development
of multivalent glycoconjugates, biosensors, glycoarrays, carbohydrate-decorated biomaterials
for regenerative medicine, and glyconanoparticles. This review aims to provide the reader with a general
overview of the different carbohydrate carrier systems that have been developed as tools in different
medicinal chemistry approaches relying on carbohydrate-protein interactions. Given the extent of
this topic, the present review will focus on selected examples that highlight the advancements and potentialities
offered by this specific area of research, rather than being an exhaustive literature survey of
any specific glyco-functionalized system.
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Affiliation(s)
- Mattia Vacchini
- Department of Biotechnology and Biosciences, University of Milano-Bicocca Milano, Italy
| | - Rana Edwards
- Department of Biotechnology and Biosciences, University of Milano-Bicocca Milano, Italy
| | - Roberto Guizzardi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca Milano, Italy
| | - Alessandro Palmioli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca Milano, Italy
| | - Carlotta Ciaramelli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca Milano, Italy
| | - Alice Paiotta
- Department of Biotechnology and Biosciences, University of Milano-Bicocca Milano, Italy
| | - Cristina Airoldi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca Milano, Italy
| | - Barbara La Ferla
- Department of Biotechnology and Biosciences, University of Milano-Bicocca Milano, Italy
| | - Laura Cipolla
- Department of Biotechnology and Biosciences, University of Milano-Bicocca Milano, Italy
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7
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Palmioli A, Sperandeo P, Polissi A, Airoldi C. Targeting Bacterial Biofilm: A New LecA Multivalent Ligand with Inhibitory Activity. Chembiochem 2019; 20:2911-2915. [DOI: 10.1002/cbic.201900383] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Indexed: 12/24/2022]
Affiliation(s)
- Alessandro Palmioli
- Department of Biotechnology and BiosciencesUniversity of Milano–Bicocca Piazza della Scienza 2 20126 Milano Italy
| | - Paola Sperandeo
- Department of Pharmacological and Biomolecular SciencesUniversity of Milano Via Balzaretti, 9/11/13 20133 Milano Italy
| | - Alessandra Polissi
- Department of Pharmacological and Biomolecular SciencesUniversity of Milano Via Balzaretti, 9/11/13 20133 Milano Italy
| | - Cristina Airoldi
- Department of Biotechnology and BiosciencesUniversity of Milano–Bicocca Piazza della Scienza 2 20126 Milano Italy
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8
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Sperandeo P, Polissi A, De Fabiani E. Fat Matters for Bugs: How Lipids and Lipid Modifications Make the Difference in Bacterial Life. EUR J LIPID SCI TECH 2019. [DOI: 10.1002/ejlt.201900204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Paola Sperandeo
- Dipartimento di Scienze Farmacologiche e BiomolecolariUniversità degli Studi di MilanoVia Balzaretti 920133MilanoItaly
| | - Alessandra Polissi
- Dipartimento di Scienze Farmacologiche e BiomolecolariUniversità degli Studi di MilanoVia Balzaretti 920133MilanoItaly
| | - Emma De Fabiani
- Dipartimento di Scienze Farmacologiche e BiomolecolariUniversità degli Studi di MilanoVia Balzaretti 920133MilanoItaly
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9
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Palmioli A, Ciaramelli C, Tisi R, Spinelli M, De Sanctis G, Sacco E, Airoldi C. Natural Compounds in Cancer Prevention: Effects of Coffee Extracts and Their Main Polyphenolic Component, 5-O-Caffeoylquinic Acid, on Oncogenic Ras Proteins. Chem Asian J 2017; 12:2457-2466. [PMID: 28719146 DOI: 10.1002/asia.201700844] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 07/17/2017] [Indexed: 01/08/2023]
Abstract
Recent epidemiological studies have demonstrated that the consumption of healthy foods that are particularly rich in polyphenols might reduce the incidence of cancer and neurodegenerative diseases. In particular, chlorogenic acids (CGAs) occur ubiquitously in food and represent the most abundant polyphenols in the human diet. A number of beneficial biological effects of CGAs, such as anti-inflammatory activity, anti-carcinogenic activity, and protection against neurodegenerative diseases, have been reported. However, the molecular mechanisms at the base of these biological activities have not yet been investigated in depth. By combining NMR spectroscopy, molecular docking, surface plasmon resonance and ex vivo assays of the Ras-dependent breast cancer cell line MDA-MB-231, we contribute to the elucidation of the molecular basis of the activity of CGAs and natural extracts from green and roasted coffee beans as chemoprotective dietary supplements.
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Affiliation(s)
- Alessandro Palmioli
- Department of Biotechnology and Biosciences, Università degli Studi di Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Carlotta Ciaramelli
- Department of Biotechnology and Biosciences, Università degli Studi di Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Renata Tisi
- Department of Biotechnology and Biosciences, Università degli Studi di Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy.,NeuroMI Milan Center for Neuroscience, University of Milano-Bicocca, 20126, Milano, Italy
| | - Michela Spinelli
- Department of Biotechnology and Biosciences, Università degli Studi di Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Gaia De Sanctis
- Department of Biotechnology and Biosciences, Università degli Studi di Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Elena Sacco
- Department of Biotechnology and Biosciences, Università degli Studi di Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy.,SysBio Center of Systems Biology, Piazza della Scienza 2, 20126, Milan, Italy
| | - Cristina Airoldi
- Department of Biotechnology and Biosciences, Università degli Studi di Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy.,NeuroMI Milan Center for Neuroscience, University of Milano-Bicocca, 20126, Milano, Italy.,SysBio Center of Systems Biology, Piazza della Scienza 2, 20126, Milan, Italy
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10
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Affiliation(s)
- Wei-Chih Wei
- Department of Chemistry; Fu Jen Catholic University; 24205 New Taipei City Taiwan
| | - Che-Chien Chang
- Department of Chemistry; Fu Jen Catholic University; 24205 New Taipei City Taiwan
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11
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Guzzi C, Colombo L, Luigi AD, Salmona M, Nicotra F, Airoldi C. Flavonoids and Their Glycosides as Anti-amyloidogenic Compounds: Aβ1-42 Interaction Studies to Gain New Insights into Their Potential for Alzheimer's Disease Prevention and Therapy. Chem Asian J 2016; 12:67-75. [DOI: 10.1002/asia.201601291] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Revised: 10/19/2016] [Indexed: 12/24/2022]
Affiliation(s)
- Cinzia Guzzi
- Department of Biotecnology and Bioscience; University of Milano-Bicocca; Piazza della Scienza 2 I-20126 Milan Italy
| | - Laura Colombo
- Department Biochemistry and Molecular Pharmacology; IRCCS-Istituto di Ricerche Farmacologiche “Mario Negri”; Via Giuseppe La Masa, 19 20156 Milan Italy
| | - Ada De Luigi
- Department Biochemistry and Molecular Pharmacology; IRCCS-Istituto di Ricerche Farmacologiche “Mario Negri”; Via Giuseppe La Masa, 19 20156 Milan Italy
| | - Mario Salmona
- Department Biochemistry and Molecular Pharmacology; IRCCS-Istituto di Ricerche Farmacologiche “Mario Negri”; Via Giuseppe La Masa, 19 20156 Milan Italy
| | - Francesco Nicotra
- Department of Biotecnology and Bioscience; University of Milano-Bicocca; Piazza della Scienza 2 I-20126 Milan Italy
- Milan Center of Neuroscience (NeuroMI); 20126 Milan Italy
| | - Cristina Airoldi
- Department of Biotecnology and Bioscience; University of Milano-Bicocca; Piazza della Scienza 2 I-20126 Milan Italy
- Milan Center of Neuroscience (NeuroMI); 20126 Milan Italy
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12
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Sperandeo P, Martorana AM, Polissi A. Lipopolysaccharide biogenesis and transport at the outer membrane of Gram-negative bacteria. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1862:1451-1460. [PMID: 27760389 DOI: 10.1016/j.bbalip.2016.10.006] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 10/11/2016] [Accepted: 10/13/2016] [Indexed: 01/10/2023]
Abstract
The outer membrane (OM) of Gram-negative bacteria is an asymmetric lipid bilayer containing a unique glycolipid, lipopolysaccharide (LPS) in its outer leaflet. LPS molecules confer to the OM peculiar permeability barrier properties enabling Gram-negative bacteria to exclude many toxic compounds, including clinically useful antibiotics, and to survive harsh environments. Transport of LPS poses several problems to the cells due to the amphipatic nature of this molecule. In this review we summarize the current knowledge on the LPS transport machinery, discuss the challenges associated with this process and present the solutions that bacterial cells have evolved to address the problem of LPS transport and assembly at the cell surface. Finally, we discuss how knowledge on LPS biogenesis can be translated for the development of novel antimicrobial therapies. This article is part of a Special Issue entitled: Bacterial Lipids edited by Russell E. Bishop.
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Affiliation(s)
- Paola Sperandeo
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy.
| | - Alessandra M Martorana
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Milan, Italy
| | - Alessandra Polissi
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy.
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13
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Ferri E, Galimberti A, Casiraghi M, Airoldi C, Ciaramelli C, Palmioli A, Mezzasalma V, Bruni I, Labra M. Towards a Universal Approach Based on Omics Technologies for the Quality Control of Food. BIOMED RESEARCH INTERNATIONAL 2015; 2015:365794. [PMID: 26783518 PMCID: PMC4691458 DOI: 10.1155/2015/365794] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 11/19/2015] [Indexed: 12/03/2022]
Abstract
In the last decades, food science has greatly developed, turning from the consideration of food as mere source of energy to a growing awareness on its importance for health and particularly in reducing the risk of diseases. Such vision led to an increasing attention towards the origin and quality of raw materials as well as their derived food products. The continuous advance in molecular biology allowed setting up efficient and universal omics tools to unequivocally identify the origin of food items and their traceability. In this review, we considered the application of a genomics approach known as DNA barcoding in characterizing the composition of foodstuffs and its traceability along the food supply chain. Moreover, metabolomics analytical strategies based on Nuclear Magnetic Resonance (NMR) and Mass Spectroscopy (MS) were discussed as they also work well in evaluating food quality. The combination of both approaches allows us to define a sort of molecular labelling of food that is easily understandable by the operators involved in the food sector: producers, distributors, and consumers. Current technologies based on digital information systems such as web platforms and smartphone apps can facilitate the adoption of such molecular labelling.
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Affiliation(s)
- Emanuele Ferri
- FEM2 Ambiente s.r.l., P.za della Scienza 2, 20126 Milan, Italy
| | - Andrea Galimberti
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.za della Scienza 2, 20126 Milan, Italy
| | - Maurizio Casiraghi
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.za della Scienza 2, 20126 Milan, Italy
| | - Cristina Airoldi
- BioNMR Lab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.za della Scienza 2, 20126 Milan, Italy
| | - Carlotta Ciaramelli
- BioNMR Lab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.za della Scienza 2, 20126 Milan, Italy
| | - Alessandro Palmioli
- FEM2 Ambiente s.r.l., P.za della Scienza 2, 20126 Milan, Italy
- BioNMR Lab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.za della Scienza 2, 20126 Milan, Italy
| | - Valerio Mezzasalma
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.za della Scienza 2, 20126 Milan, Italy
| | - Ilaria Bruni
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.za della Scienza 2, 20126 Milan, Italy
| | - Massimo Labra
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.za della Scienza 2, 20126 Milan, Italy
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14
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Airoldi C, D'Orazio G, Richichi B, Guzzi C, Baldoneschi V, Colombo L, Salmona M, Nativi C, Nicotra F, La Ferla B. Structural Modifications ofcis-Glycofused Benzopyran Compounds and Their Influence on the Binding to Amyloid-β Peptide. Chem Asian J 2015; 11:299-309. [DOI: 10.1002/asia.201501114] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Indexed: 01/22/2023]
Affiliation(s)
- Cristina Airoldi
- Department of Biotecnology and Bioscience (Btbs); University of Milano-Bicocca; Piazza della Scienza 2 I-20126 Milan Italy
| | - Giuseppe D'Orazio
- Department of Biotecnology and Bioscience (Btbs); University of Milano-Bicocca; Piazza della Scienza 2 I-20126 Milan Italy
| | - Barbara Richichi
- Department of Chemistry “Ugo Schiff”; University of Florence; Via della Lastruccia 3-13 I-50019 Sesto Fiorentino (FI) Italy
| | - Cinzia Guzzi
- Department of Biotecnology and Bioscience (Btbs); University of Milano-Bicocca; Piazza della Scienza 2 I-20126 Milan Italy
| | - Veronica Baldoneschi
- Department of Chemistry “Ugo Schiff”; University of Florence; Via della Lastruccia 3-13 I-50019 Sesto Fiorentino (FI) Italy
| | - Laura Colombo
- Department Biochemistry and Molecular Pharmacology; IRCCS-Istituto di Ricerche Farmacologiche “Mario Negri”; Via Giuseppe La Masa, 19 20156 Milano Italy
| | - Mario Salmona
- Department Biochemistry and Molecular Pharmacology; IRCCS-Istituto di Ricerche Farmacologiche “Mario Negri”; Via Giuseppe La Masa, 19 20156 Milano Italy
| | - Cristina Nativi
- Department of Chemistry “Ugo Schiff”; University of Florence; Via della Lastruccia 3-13 I-50019 Sesto Fiorentino (FI) Italy
| | - Francesco Nicotra
- Department of Biotecnology and Bioscience (Btbs); University of Milano-Bicocca; Piazza della Scienza 2 I-20126 Milan Italy
| | - Barbara La Ferla
- Department of Biotecnology and Bioscience (Btbs); University of Milano-Bicocca; Piazza della Scienza 2 I-20126 Milan Italy
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Bonanomi M, Visentin C, Natalello A, Spinelli M, Vanoni M, Airoldi C, Regonesi ME, Tortora P. How Epigallocatechin-3-gallate and Tetracycline Interact with the Josephin Domain of Ataxin-3 and Alter Its Aggregation Mode. Chemistry 2015; 21:18383-93. [PMID: 26538519 DOI: 10.1002/chem.201503086] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Indexed: 12/17/2022]
Abstract
Epigallocatechin-3-gallate (EGCG) and tetracycline are two known inhibitors of amyloid aggregation able to counteract the fibrillation of most of the proteins involved in neurodegenerative diseases. We have recently investigated their effect on ataxin-3 (AT3), the polyglutamine-containing protein responsible for spinocerebellar ataxia type 3. We previously showed that EGCG and tetracycline can contrast the aggregation process and toxicity of expanded AT3, although by different mechanisms. Here, we have performed further experiments by using the sole Josephin domain (JD) to further elucidate the mechanism of action of the two compounds. By protein solubility assays and FTIR spectroscopy we have first observed that EGCG and tetracycline affect the JD aggregation essentially in the same way displayed when acting on the full-length expanded AT3. Then, by saturation transfer difference (STD) NMR experiments, we have shown that EGCG binds both the monomeric and the oligomeric JD form, whereas tetracycline can only interact with the oligomeric one. Surface plasmon resonance (SPR) analysis has confirmed the capability of the sole EGCG to bind monomeric JD, although with a KD value suggestive for a non-specific interaction. Our investigations provide new details on the JD interaction with EGCG and tetracycline, which could explain the different mechanisms by which the two compounds reduce the toxicity of AT3.
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Affiliation(s)
- Marcella Bonanomi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano (Italy)
| | - Cristina Visentin
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano (Italy)
| | - Antonino Natalello
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano (Italy).,Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia (CNISM), UdR Milano-Bicocca, Milano (Italy).,Milan Center of Neuroscience (NeuroMI), 20126 Milano (Italy)
| | - Michela Spinelli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano (Italy).,SysBio Centre for Systems Biology, Milano and Rome (Italy)
| | - Marco Vanoni
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano (Italy).,Milan Center of Neuroscience (NeuroMI), 20126 Milano (Italy).,SysBio Centre for Systems Biology, Milano and Rome (Italy)
| | - Cristina Airoldi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano (Italy). .,Milan Center of Neuroscience (NeuroMI), 20126 Milano (Italy). .,SysBio Centre for Systems Biology, Milano and Rome (Italy).
| | - Maria E Regonesi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano (Italy). .,Milan Center of Neuroscience (NeuroMI), 20126 Milano (Italy).
| | - Paolo Tortora
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano (Italy).,Milan Center of Neuroscience (NeuroMI), 20126 Milano (Italy)
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Sironi E, Colombo L, Lompo A, Messa M, Bonanomi M, Regonesi ME, Salmona M, Airoldi C. Natural Compounds against Neurodegenerative Diseases: Molecular Characterization of the Interaction of Catechins from Green Tea with Aβ1–42, PrP106–126, and Ataxin‐3 Oligomers. Chemistry 2014; 20:13793-800. [DOI: 10.1002/chem.201403188] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Indexed: 12/31/2022]
Affiliation(s)
- Erika Sironi
- Department of Biotechnology and Biosciences University of Milano‐Bicocca, P.zza della Scienza, 2, 20126, Milano (Italy), Fax: (+39) 02‐6448‐3565
| | - Laura Colombo
- Department Biochemistry and Molecular Pharmacology, IRCCS‐Istituto di Ricerche Farmacologiche “Mario Negri”, Via Giuseppe La Masa, 19 20156 Milano (Italy)
| | - Angela Lompo
- Department of Biotechnology and Biosciences University of Milano‐Bicocca, P.zza della Scienza, 2, 20126, Milano (Italy), Fax: (+39) 02‐6448‐3565
| | - Massimo Messa
- Department Biochemistry and Molecular Pharmacology, IRCCS‐Istituto di Ricerche Farmacologiche “Mario Negri”, Via Giuseppe La Masa, 19 20156 Milano (Italy)
| | - Marcella Bonanomi
- Department of Biotechnology and Biosciences University of Milano‐Bicocca, P.zza della Scienza, 2, 20126, Milano (Italy), Fax: (+39) 02‐6448‐3565
| | - Maria Elena Regonesi
- Department of Statistics and Quantitative Methods, University of Milano‐Bicocca, Via Bicocca degli Arcimboldi, 8, 20126, Milano (Italy)
| | - Mario Salmona
- Department Biochemistry and Molecular Pharmacology, IRCCS‐Istituto di Ricerche Farmacologiche “Mario Negri”, Via Giuseppe La Masa, 19 20156 Milano (Italy)
| | - Cristina Airoldi
- Department of Biotechnology and Biosciences University of Milano‐Bicocca, P.zza della Scienza, 2, 20126, Milano (Italy), Fax: (+39) 02‐6448‐3565
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Merlo S, Sironi E, Colombo L, Cardona F, Martorana AM, Salmona M, La Ferla B, Airoldi C. Cis-Glyco-Fused Benzopyran Derivatives as Hit Compounds for the Development of Therapeutic and Diagnostic Tools against Neurodegenerative Diseases. Chempluschem 2014. [DOI: 10.1002/cplu.201400035] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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18
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Cipolla L, Airoldi C, Sperandeo P, Gianera S, Polissi A, Nicotra F, Gabrielli L. Synthesis and biological evaluation of arabinose 5-phosphate mimics modified at position five. Carbohydr Res 2014; 389:186-91. [DOI: 10.1016/j.carres.2014.01.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 12/31/2013] [Accepted: 01/08/2014] [Indexed: 01/10/2023]
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19
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Gabrielli L, Merlo S, Airoldi C, Sperandeo P, Gianera S, Polissi A, Nicotra F, Holler TP, Woodard RW, Cipolla L. Arabinose 5-phosphate isomerase as a target for antibacterial design: Studies with substrate analogues and inhibitors. Bioorg Med Chem 2014; 22:2576-83. [DOI: 10.1016/j.bmc.2013.08.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Revised: 07/18/2013] [Accepted: 08/05/2013] [Indexed: 01/25/2023]
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20
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Gabrielli L, Airoldi C, Sperandeo P, Gianera S, Polissi A, Nicotra F, Cipolla L. Phosphonate Analogues of Arabinose 5-Phosphate: Putative Ligands for Arabinose 5-Phosphate Isomerases. European J Org Chem 2013. [DOI: 10.1002/ejoc.201300887] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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21
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Smyth KM, Marchant A. Conservation of the 2-keto-3-deoxymanno-octulosonic acid (Kdo) biosynthesis pathway between plants and bacteria. Carbohydr Res 2013; 380:70-5. [DOI: 10.1016/j.carres.2013.07.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 07/02/2013] [Accepted: 07/12/2013] [Indexed: 01/22/2023]
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22
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Fluorescent amyloid β-peptide ligand derivatives as potential diagnostic tools for Alzheimer’s disease. PURE APPL CHEM 2013. [DOI: 10.1351/pac-con-12-11-07] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Aβ-peptide ligands based on a cis-glycofused benzopyran structure have been fluorescently labeled using coumarine derivatives. Among the synthesized compounds, two conserved their binding ability to β-amyloid peptides, as shown by NMR experiments. Moreover, exploiting its fluorescent property, it was demonstrated that one of such compounds was able to cross an in vitro model of blood–brain barrier (BBB) and to stain Aβ‑deposits.
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Airoldi C, Giovannardi S, La Ferla B, Jiménez-Barbero J, Nicotra F. Saturation Transfer Difference NMR Experiments of Membrane Proteins in Living Cells under HR-MAS Conditions: The Interaction of the SGLT1 Co-transporter with Its Ligands. Chemistry 2011; 17:13395-9. [DOI: 10.1002/chem.201102181] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Indexed: 12/13/2022]
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24
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Airoldi C, Sommaruga S, Merlo S, Sperandeo P, Cipolla L, Polissi A, Nicotra F. Targeting Bacterial Membranes: Identification of Pseudomonas aeruginosaD-Arabinose-5P Isomerase and NMR Characterisation of its Substrate Recognition and Binding Properties. Chembiochem 2011; 12:719-27. [DOI: 10.1002/cbic.201000754] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Indexed: 11/10/2022]
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25
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Airoldi C, Cardona F, Sironi E, Colombo L, Salmona M, Silva A, Nicotra F, La Ferla B. cis-Glyco-fused benzopyran compounds as new amyloid-β peptide ligands. Chem Commun (Camb) 2011; 47:10266-8. [DOI: 10.1039/c1cc13046c] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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26
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Cipolla L, Gabrielli L, Bini D, Russo L, Shaikh N. Kdo: a critical monosaccharide for bacteria viability. Nat Prod Rep 2010; 27:1618-29. [DOI: 10.1039/c004750n] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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